File: test-example

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snpomatic 1.0-7
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#!/bin/sh
# autopkgtest check: Run simulated test data through snpomatic
# Author: Sascha Steinbiss <sascha@steinbiss.name>
set -e

ORIGDIR=$(pwd)
DATADIR=$ORIGDIR/debian/tests/
WORKDIR=$(mktemp -d)

trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
cd $WORKDIR

cp $DATADIR/ref.fasta .
wgsim -N 10000 -r 0.01 -S 42 \
  ref.fasta \
  reads.1.fq \
  reads.2.fq
findknownsnps --genome=ref.fasta \
  --fastq=reads.1.fq \
  --gffout=out.gff \
  --fastq2=reads.2.fq

[ -s out.gff ]